Cited by 3RNA Interference and Gene DeliveryRNA and protein synthesis mechanismsRNA modifications and cancer

A comprehensive analysis of the use of nucleoside analogues in RNA therapeutics

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Kukushkina-Zvezdova, Alisa A., Zherebtsova, Anna A., Telegina, Darya V., Skvortsov, Ivan A., Ivanov, Roman A., Reshetnikov, Vasiliy V.·2026·Journal of Translational Medicine

Abstract

BACKGROUND: mRNA therapeutics represent a promising frontier in the development of vaccines, anti-cancer treatments, and gene replacement therapies. The mRNA platform facilitates the rapid design of effective and safe candidates. However, native mRNA molecules are inherently characterized by limited stability and high reactogenicity, which may compromise their in vivo efficacy. The incorporation of modified nucleoside analogues can address these challenges by extending the mRNA half-life and subsequently enhancing protein expression. MAIN BODY: Despite the discovery and widespread adoption of pseudouridine (Ψ) and N1-methylpseudouridine (m1Ψ) in mRNA therapeutics, these modifications have not fully addressed all inherent limitations of mRNA-based platforms. Consequently, identifying novel nucleoside analogues, their combinations, and alternative therapeutic strategies remains a critical area of research. This review provides a comprehensive overview of how commonly used nucleoside analogues influence mRNA stability, translation, and immunogenicity, while also discussing their natural distribution patterns in native mRNA. Furthermore, we examine experimental in vitro and in vivo data regarding the application of non-canonical nucleosides in cell and animal models and evaluate the future prospects of modified mRNA-based therapies. CONCLUSION: In conclusion, this review provides an extensive analysis of the properties of modified nucleosides employed in mRNA formulations and characterizes their impact on the overall efficacy of mRNA-based therapeutics in detail.

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  • Inclusion of specific untranslated regions is a promising strategy to enhance stability and efficacy of mRNA therapeutics.

    “Recent studies demonstrate that, in addition to the incorporation of modified nucleosides, the inclusion of specific untranslated regions represents a highly promising strategy to enhance the stability and efficacy of mRNA therapeutics [12][13][14][15][16].”

    From Identification of novel 5’ UTR variants for enhanced mRNA translation and vaccine immunogenicity (2026) · cites this paper as [16]

    In “Synthesis of mRNA with region-specific modifications” (page unavailable), the review says that optimizing mRNA secondary structure for stability and translatability takes UTR structures into account. It does not specifically say that including particular untranslated regions enhances therapeutic stability and efficacy; its proposed strategy concerns sequence or structural optimization and region-specific nucleoside modifications. (LLM, conf=0.81)

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  1. [1]Deyhimfar R, Izady M, Shoghi M, Kazazi MH, Ghazvini ZF, Nazari H, et al. The clinical impact of mRNA therapeutics in the treatment of cancers, infections, genetic disorders, and autoimmune diseases. Heliyon. 2024. 10.1016/j.heliyon.2024.e26971. 38486748 PMC10937594 · DOI
  2. [2]Pateev I, Seregina K, Ivanov R, Reshetnikov V. Biodistribution of RNA Vaccines and of Their Products: Evidence from Human and Animal Studies. Biomedicines. 2023. 10.3390/biomedicines12010059. 38255166 PMC10812935 · DOI
  3. [3]Self WH, Tenforde MW, Rhoads JP, Gaglani M, Ginde AA, Douin DJ, et al. Comparative Effectiveness of Moderna, Pfizer-BioNTech, and Janssen (Johnson & Johnson) Vaccines in Preventing COVID-19 Hospitalizations Among Adults Without Immunocompromising Conditions — United States, March–August 2021. MMWR Morb Mortal Wkly Rep. 2021. 10.15585/mmwr.mm7038e1. 34555004 PMC8459899 · DOI · Paper page
  4. [4]Karikó K, Buckstein M, Ni H, Weissman D. Suppression of RNA Recognition by Toll-like Receptors: The Impact of Nucleoside Modification and the Evolutionary Origin of RNA. Immunity. 2005. 10.1016/j.immuni.2005.06.008. 16111635 · DOI · Paper page
  5. [5]McCown PJ, Ruszkowska A, Kunkler CN, Breger K, Hulewicz JP, Wang MC, et al. Naturally occurring modified ribonucleosides. WIREs RNA. 2020. 10.1002/wrna.1595. 32301288 PMC7694415 · DOI
  6. [6]Jones JD, Monroe J, Koutmou KS. A molecular-level perspective on the frequency, distribution, and consequences of messenger RNA modifications. WIREs RNA. 2020. 10.1002/wrna.1586. 31960607 PMC8243748 · DOI
  7. [7]Cappannini A, Ray A, Purta E, Mukherjee S, Boccaletto P, Moafinejad SN, et al. MODOMICS: a database of RNA modifications and related information. 2023 update. Nucleic Acids Res. 2024. 10.1093/nar/gkad1083. 38015436 PMC10767930 · DOI
  8. [8]Boccaletto P, Machnicka MA, Purta E, Piątkowski P, Bagiński B, Wirecki TK, et al. MODOMICS: a database of RNA modification pathways. 2017 update. Nucleic Acids Res. 2018. 10.1093/nar/gkx1030. 29106616 PMC5753262 · DOI
  9. [9]Wurtmann EJ, Wolin SL. RNA under attack: Cellular handling of RNA damage. Crit Rev Biochem Mol Biol. 2009. 10.1080/10409230802594043. 19089684 PMC2656420 · DOI
  10. [10]McMahon M, editor. RNA Modifications. New York, NY: Springer US; 2021.
  11. [11]Gilbert WV, Bell TA, Schaening C. Messenger RNA modifications: Form, distribution, and function. Science. 2016. 10.1126/science.aad8711. 27313037 PMC5094196 · DOI
  12. [12]Franco MK, Koutmou KS. Chemical modifications to mRNA nucleobases impact translation elongation and termination. Biophys Chem. 2022. 10.1016/j.bpc.2022.106780. 35313212 PMC9373004 · DOI
  13. [13]Finet O, Yague-Sanz C, Krüger LK, Tran P, Migeot V, Louski M, et al. Transcription-wide mapping of dihydrouridine reveals that mRNA dihydrouridylation is required for meiotic chromosome segregation. Mol Cell. 2022. 10.1016/j.molcel.2021.11.003. 34798057 PMC8792297 · DOI
  14. [14]Grozhik AV, Jaffrey SR. Distinguishing RNA modifications from noise in epitranscriptome maps. Nat Chem Biol. 2018. 10.1038/nchembio.2546. 29443978 · DOI
  15. [15]Yan LL, Zaher HS. How do cells cope with RNA damage and its consequences? J Biol Chem. 2019. 10.1074/jbc.REV119.006513. 31439666 PMC6791314 · DOI
  16. [16]Desrosiers R, Friderici K, Rottman F. Identification of Methylated Nucleosides in Messenger RNA from Novikoff Hepatoma Cells. Proc Natl Acad Sci. 1974. 10.1073/pnas.71.10.3971. 4372599 PMC434308 · DOI
  17. [17]Yang Y, Wang L, Han X, Yang W-L, Zhang M, Ma H-L, et al. RNA 5-Methylcytosine Facilitates the Maternal-to-Zygotic Transition by Preventing Maternal mRNA Decay. Mol Cell. 2019. 10.1016/j.molcel.2019.06.033. 31399345 · DOI
  18. [18]Zou F, Tu R, Duan B, Yang Z, Ping Z, Song X, et al. Drosophila YBX1 homolog YPS promotes ovarian germ line stem cell development by preferentially recognizing 5-methylcytosine RNAs. Proc Natl Acad Sci. 2020. 10.1073/pnas.1910862117. 32015133 PMC7035628 · DOI
  19. [19]Hoernes TP, Hüttenhofer A, Erlacher MD. mRNA modifications: Dynamic regulators of gene expression? RNA Biol. 2016. 10.1080/15476286.2016.1203504. 27351916 PMC5014007 · DOI
  20. [20]Dominissini D, Nachtergaele S, Moshitch-Moshkovitz S, Peer E, Kol N, Ben-Haim MS, et al. The dynamic N1-methyladenosine methylome in eukaryotic messenger RNA. Nature. 2016. 10.1038/nature16998. 26863196 PMC4842015 · DOI
  21. [21]Fernández IS, Ng CL, Kelley AC, Wu G, Yu Y-T, Ramakrishnan V. Unusual base pairing during the decoding of a stop codon by the ribosome. Nature. 2013. 10.1038/nature12302. 23812587 PMC3732562 · DOI
  22. [22]Hoernes TP, Clementi N, Faserl K, Glasner H, Breuker K, Lindner H, et al. Nucleotide modifications within bacterial messenger RNAs regulate their translation and are able to rewire the genetic code. Nucleic Acids Res. 2016. 10.1093/nar/gkv1182. 26578598 PMC4737146 · DOI
  23. [23]Harcourt EM, Kietrys AM, Kool ET. Chemical and structural effects of base modifications in messenger RNA. Nature. 2017. 10.1038/nature21351. 28102265 PMC5498787 · DOI
  24. [24]Jonkhout N, Tran J, Smith MA, Schonrock N, Mattick JS, Novoa EM. The RNA modification landscape in human disease. RNA. 2017. 10.1261/rna.063503.117. 28855326 PMC5688997 · DOI
  25. [25]Du T, Rao S, Wu L, Ye N, Liu Z, Hu H, et al. An association study of the m6A genes with major depressive disorder in Chinese Han population. J Affect Disord. 2015. 10.1016/j.jad.2015.05.025. 26047305 · DOI · Paper page
  26. [26]Ben-Haim MS, Moshitch-Moshkovitz S, Rechavi G. FTO: linking m6A demethylation to adipogenesis. Cell Res. 2015. 10.1038/cr.2014.162. 25475057 PMC4650590 · DOI
  27. [27]Bumcrot D, Manoharan M, Koteliansky V, Sah DWY. RNAi therapeutics: a potential new class of pharmaceutical drugs. Nat Chem Biol. 2006. 10.1038/nchembio839. 17108989 PMC7097247 · DOI
  28. [28]Nance KD, Meier JL. Modifications in an Emergency: The Role of N1-Methylpseudouridine in COVID-19 Vaccines. ACS Cent Sci. 2021. 10.1021/acscentsci.1c00197. 34075344 PMC8043204 · DOI · Paper page
  29. [30]Dhurbachandra Singh C, Morshed Alom K, Kumar Kannan D, Simander Singh T, Samantaray S, Siddappa Ravi Kumara G, et al. mRNA incorporation of C(5)-halogenated pyrimidine ribonucleotides and induced high expression of corresponding protein for the development of mRNA vaccine. Bioorg Chem. 2023. 10.1016/j.bioorg.2023.106897. 37793265 · DOI
  30. [31]Kawaguchi D, Kodama A, Abe N, Takebuchi K, Hashiya F, Tomoike F, et al. Phosphorothioate Modification of mRNA Accelerates the Rate of Translation Initiation to Provide More Efficient Protein Synthesis. Angew Chem Int Ed. 2020. 10.1002/anie.202007111. 32627275 · DOI
  31. [32]Fu Y, Dominissini D, Rechavi G, He C. Gene expression regulation mediated through reversible m6A RNA methylation. Nat Rev Genet. 2014. 10.1038/nrg3724. 24662220 · DOI
  32. [33]Deng X, Chen K, Luo G-Z, Weng X, Ji Q, Zhou T, et al. Widespread occurrence of N 6 -methyladenosine in bacterial mRNA. Nucleic Acids Res. 2015. 10.1093/nar/gkv596. 26068471 PMC4513869 · DOI
  33. [34]Jia G, Fu Y, He C. Reversible RNA adenosine methylation in biological regulation. Trends Genet. 2013. 10.1016/j.tig.2012.11.003. 23218460 PMC3558665 · DOI
  34. [35]Tuck MT. The formation of internal 6-methyladenine residues in eucaryotic messenger rna. Int J Biochem. 1992. 10.1016/0020-711X(92)90028-Y. 1551452 · DOI
  35. [36]Lavi U, Fernandez-Mufioz R, Darnell JE. Content of N-6 methyl adenylic acid in heterogeneous nuclear and messenger RNA of HeLa cells. Nucleic Acids Res. 1977. 10.1093/nar/4.1.63. 866178 PMC342409 · DOI
  36. [37]Sommer S, Salditt-Georgieff M, Bachenheimer S, Darnell JE, Furuichi Y, Morgan M, et al. The methylation of adenovirus-specific nuclear and cytoplasmic RNA. Nucleic Acids Res. 1976. 10.1093/nar/3.3.749. 1272797 PMC342938 · DOI
  37. [38]Jia G, Fu Y, Zhao X, Dai Q, Zheng G, Yang Y, et al. N6-Methyladenosine in nuclear RNA is a major substrate of the obesity-associated FTO. Nat Chem Biol. 2011. 10.1038/nchembio.687. 22002720 PMC3218240 · DOI · Paper page
  38. [39]Zheng G, Dahl JA, Niu Y, Fedorcsak P, Huang C-M, Li CJ, et al. ALKBH5 Is a Mammalian RNA Demethylase that Impacts RNA Metabolism and Mouse Fertility. Mol Cell. 2013. 10.1016/j.molcel.2012.10.015. 23177736 PMC3646334 · DOI · Paper page
  39. [40]Dominissini D, Moshitch-Moshkovitz S, Schwartz S, Salmon-Divon M, Ungar L, Osenberg S, et al. Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq. Nature. 2012. 10.1038/nature11112. 22575960 · DOI · Paper page
  40. [41]Meyer KD, Saletore Y, Zumbo P, Elemento O, Mason CE, Jaffrey SR. Comprehensive Analysis of mRNA Methylation Reveals Enrichment in 3′ UTRs and near Stop Codons. Cell. 2012. 10.1016/j.cell.2012.05.003. 22608085 PMC3383396 · DOI · Paper page
  41. [42]Wang X, Lu Z, Gomez A, Hon GC, Yue Y, Han D, et al. N6-methyladenosine-dependent regulation of messenger RNA stability. Nature. 2014. 10.1038/nature12730. 24284625 PMC3877715 · DOI · Paper page
  42. [43]Du H, Zhao Y, He J, Zhang Y, Xi H, Liu M, et al. YTHDF2 destabilizes m6A-containing RNA through direct recruitment of the CCR4–NOT deadenylase complex. Nat Commun. 2016. 10.1038/ncomms12626. 27558897 PMC5007331 · DOI
  43. [44]Heck AM, Wilusz J. The Interplay between the RNA Decay and Translation Machinery in Eukaryotes. Cold Spring Harb Perspect Biol. 2018. 10.1101/cshperspect.a032839. 29311343 PMC5932591 · DOI
  44. [45]Fry NJ, Law BA, Ilkayeva OR, Holley CL, Mansfield KD. N 6 -methyladenosine is required for the hypoxic stabilization of specific mRNAs. RNA. 2017. 10.1261/rna.061044.117. 28611253 PMC5558913 · DOI
  45. [46]Li Z, Weng H, Su R, Weng X, Zuo Z, Li C, et al. FTO Plays an Oncogenic Role in Acute Myeloid Leukemia as a N 6 -Methyladenosine RNA Demethylase. Cancer Cell. 2017. 10.1016/j.ccell.2016.11.017. 28017614 PMC5234852 · DOI
  46. [47]Huang H, Weng H, Sun W, Qin X, Shi H, Wu H, et al. Recognition of RNA N6-methyladenosine by IGF2BP proteins enhances mRNA stability and translation. Nat Cell Biol. 2018. 10.1038/s41556-018-0045-z. 29476152 PMC5826585 · DOI · Paper page
  47. [48]Zhang F, Kang Y, Wang M, Li Y, Xu T, Yang W, et al. Fragile X mental retardation protein modulates the stability of its m6A-marked messenger RNA targets. Hum Mol Genet. 2018. 10.1093/hmg/ddy292. 30107516 PMC6216232 · DOI
  48. [49]Edupuganti RR, Geiger S, Lindeboom RGH, Shi H, Hsu PJ, Lu Z, et al. N6-methyladenosine (m6A) recruits and repels proteins to regulate mRNA homeostasis. Nat Struct Mol Biol. 2017. 10.1038/nsmb.3462. 28869609 PMC5725193 · DOI
  49. [50]Visvanathan A, Patil V, Arora A, Hegde AS, Arivazhagan A, Santosh V, et al. Essential role of METTL3-mediated m6A modification in glioma stem-like cells maintenance and radioresistance. Oncogene. 2018. 10.1038/onc.2017.351. 28991227 · DOI
  50. [51]Wang Y, Li Y, Toth JI, Petroski MD, Zhang Z, Zhao JC. N6-methyladenosine modification destabilizes developmental regulators in embryonic stem cells. Nat Cell Biol. 2014. 10.1038/ncb2902. 24394384 PMC4640932 · DOI
  51. [52]Wu R, Li A, Sun B, Sun J-G, Zhang J, Zhang T, et al. A novel m6A reader Prrc2a controls oligodendroglial specification and myelination. Cell Res. 2019. 10.1038/s41422-018-0113-8. 30514900 PMC6318280 · DOI · Paper page
  52. [53]Arribas-Hernández L, Bressendorff S, Hansen MH, Poulsen C, Erdmann S, Brodersen P. An m 6 A-YTH Module Controls Developmental Timing and Morphogenesis in Arabidopsis. Plant Cell. 2018. 10.1105/tpc.17.00833. 29643069 PMC6002192 · DOI
  53. [54]Wei L-H, Song P, Wang Y, Lu Z, Tang Q, Yu Q, et al. The m 6 A Reader ECT2 Controls Trichome Morphology by Affecting mRNA Stability in Arabidopsis. Plant Cell. 2018. 10.1105/tpc.17.00934. 29716990 PMC6002187 · DOI
  54. [55]Duan H-C, Wei L-H, Zhang C, Wang Y, Chen L, Lu Z, et al. ALKBH10B Is an RNA N 6 -Methyladenosine Demethylase Affecting Arabidopsis Floral Transition. Plant Cell. 2017. 10.1105/tpc.16.00912. 29180595 PMC5757257 · DOI
  55. [56]Roost C, Lynch SR, Batista PJ, Qu K, Chang HY, Kool ET. Structure and Thermodynamics of N 6 -Methyladenosine in RNA: A Spring-Loaded Base Modification. J Am Chem Soc. 2015. 10.1021/ja513080v. 26087989 · DOI
  56. [57]Spitale RC, Flynn RA, Zhang QC, Crisalli P, Lee B, Jung J-W, et al. Structural imprints in vivo decode RNA regulatory mechanisms. Nature. 2015. 10.1038/nature14263. 25799993 PMC4376618 · DOI
  57. [58]Agris PF. Bringing order to translation: the contributions of transfer RNA anticodon-domain modifications. EMBO Rep. 2008. 10.1038/embor.2008.104. 18552770 PMC2475317 · DOI
  58. [59]Hayashi Y, Osawa S, Miura K. The methyl groups in ribosomal RNA from Escherichia coli. Biochim Biophys Acta. 1966. 10.1016/0005-2787(66)90067-0. 5337971 · DOI
  59. [60]Noon KR, Bruenger E, McCloskey JA. Posttranscriptional Modifications in 16S and 23S rRNAs of the Archaeal Hyperthermophile Sulfolobus solfataricus. J Bacteriol. 1998. 10.1128/JB.180.11.2883-2888.1998. 9603876 PMC107253 · DOI
  60. [61]Helm M. Post-transcriptional nucleotide modification and alternative folding of RNA. Nucleic Acids Res. 2006. 10.1093/nar/gkj471. 16452298 PMC1360285 · DOI
  61. [62]Edelheit S, Schwartz S, Mumbach MR, Wurtzel O, Sorek R. Transcriptome-Wide Mapping of 5-methylcytidine RNA Modifications in Bacteria, Archaea, and Yeast Reveals m5C within Archaeal mRNAs. PLoS Genet. 2013. 10.1371/journal.pgen.1003602. 23825970 PMC3694839 · DOI
  62. [63]Squires JE, Patel HR, Nousch M, Sibbritt T, Humphreys DT, Parker BJ, et al. Widespread occurrence of 5-methylcytosine in human coding and non-coding RNA. Nucleic Acids Res. 2012. 10.1093/nar/gks144. 22344696 PMC3367185 · DOI
  63. [64]Yang X, Yang Y, Sun B-F, Chen Y-S, Xu J-W, Lai W-Y, et al. 5-methylcytosine promotes mRNA export — NSUN2 as the methyltransferase and ALYREF as an m5C reader. Cell Res. 2017. 10.1038/cr.2017.55. 28418038 PMC5594206 · DOI
  64. [65]Young JI, Hong EP, Castle JC, Crespo-Barreto J, Bowman AB, Rose MF et al. Regulation of RNA splicing by the methylation-dependent transcriptional repressor methyl-CpG binding protein 2. Proc Natl Acad Sci. 2005. 10.1073/pnas.0507856102. PMC1266160 16251272 · DOI · Paper page
  65. [66]Chen H, Yang H, Zhu X, Yadav T, Ouyang J, Truesdell SS, et al. m5C modification of mRNA serves a DNA damage code to promote homologous recombination. Nat Commun. 2020. 10.1038/s41467-020-16722-7. 32503981 PMC7275041 · DOI
  66. [67]Xue S, Xu H, Sun Z, Shen H, Chen S, Ouyang J, et al. Depletion of TRDMT1 affects 5-methylcytosine modification of mRNA and inhibits HEK293 cell proliferation and migration. Biochem Biophys Res Commun. 2019. 10.1016/j.bbrc.2019.09.098. 31570165 · DOI
  67. [68]Warren L, Manos PD, Ahfeldt T, Loh Y-H, Li H, Lau F, et al. Highly Efficient Reprogramming to Pluripotency and Directed Differentiation of Human Cells with Synthetic Modified mRNA. Cell Stem Cell. 2010. 10.1016/j.stem.2010.08.012. 20888316 PMC3656821 · DOI · Paper page
  68. [69]Squires JE, Preiss T. Function and Detection of 5-Methylcytosine in eukaryotic RNA. Epigenomics. 2010. 10.2217/epi.10.47. 22122054 · DOI
  69. [70]Trixl L, Lusser A. The dynamic RNA modification 5-methylcytosine and its emerging role as an epitranscriptomic mark. WIREs RNA. 2019. 10.1002/wrna.1510. 30311405 PMC6492194 · DOI
  70. [71]Sibbritt T, Patel HR, Preiss T. Mapping and significance of the < scp>mRNA methylome. WIREs RNA. 2013. 10.1002/wrna.1166. 23681756 · DOI
  71. [72]Huber SM, van Delft P, Mendil L, Bachman M, Smollett K, Werner F, et al. Formation and Abundance of 5-Hydroxymethylcytosine in RNA. ChemBioChem. 2015. 10.1002/cbic.201500013. 25676849 PMC4471624 · DOI
  72. [73]Khoddami V, Cairns BR. Identification of direct targets and modified bases of RNA cytosine methyltransferases. Nat Biotechnol. 2013. 10.1038/nbt.2566. 23604283 PMC3791587 · DOI
  73. [74]Chen X, Li A, Sun B-F, Yang Y, Han Y-N, Yuan X, et al. 5-methylcytosine promotes pathogenesis of bladder cancer through stabilizing mRNAs. Nat Cell Biol. 2019. 10.1038/s41556-019-0361-y. 31358969 · DOI
  74. [75]Hayrapetyan A, Grosjean H, Helm M. Effect of a quaternary pentamine on RNA stabilization and enzymatic methylation. bchm. 2009. 10.1515/BC.2009.096. 19558320 · DOI
  75. [76]Motorin Y, Helm M. tRNA Stabilization by Modified Nucleotides. Biochemistry. 2010. 10.1021/bi100408z. 20459084 · DOI
  76. [77]Schosserer M, Minois N, Angerer TB, Amring M, Dellago H, Harreither E, et al. Methylation of ribosomal RNA by NSUN5 is a conserved mechanism modulating organismal lifespan. Nat Commun. 2015. 10.1038/ncomms7158. 25635753 PMC4317494 · DOI
  77. [78]Yang L, Perrera V, Saplaoura E, Apelt F, Bahin M, Kramdi A, et al. m5C Methylation Guides Systemic Transport of Messenger RNA over Graft Junctions in Plants. Curr Biol. 2019. 10.1016/j.cub.2019.06.042. 31327714 · DOI
  78. [79]David R, Burgess A, Parker B, Li J, Pulsford K, Sibbritt T, et al. Transcriptome-Wide Mapping of RNA 5-Methylcytosine in Arabidopsis mRNAs and Noncoding RNAs. Plant Cell. 2017. 10.1105/tpc.16.00751. 28062751 PMC5385953 · DOI
  79. [80]Cui X, Liang Z, Shen L, Zhang Q, Bao S, Geng Y, et al. 5-Methylcytosine RNA Methylation in Arabidopsis Thaliana. Mol Plant. 2017. 10.1016/j.molp.2017.09.013. 28965832 · DOI
  80. [81]Roy B. Effects of mRNA Modifications on Translation: An Overview. Methods Mol Biol. 2021. 10.1007/978-1-0716-1374-0_20. 34085254 · DOI
  81. [82]Lan J, Rajan N, Bizet M, Penning A, Singh NK, Guallar D, et al. Functional role of Tet-mediated RNA hydroxymethylcytosine in mouse ES cells and during differentiation. Nat Commun. 2020. 10.1038/s41467-020-18729-6. 33009383 PMC7532169 · DOI
  82. [83]Zhao C, Hamilton T. Introns Regulate the Rate of Unstable mRNA Decay. J Biol Chem. 2007. 10.1074/jbc.M700180200. 17478421 · DOI
  83. [84]Xia M, Yan R, Wang W, Kong A, Zhang M, Miao Z, et al. The Tet2–Upf1 complex modulates mRNA stability under stress conditions. Front Genet. 2023. 10.3389/fgene.2023.1158954. 37091805 PMC10117899 · DOI
  84. [85]Riml C, Lusser A, Ennifar E, Micura R, Synthesis. Thermodynamic Properties, and Crystal Structure of RNA Oligonucleotides Containing 5-Hydroxymethylcytosine. J Org Chem. 2017. 10.1021/acs.joc.7b01171. 28707898 · DOI
  85. [86]Thalhammer A, Hansen AS, El-Sagheer AH, Brown T, Schofield CJ. Hydroxylation of methylated CpG dinucleotides reverses stabilisation of DNA duplexes by cytosine 5-methylation. Chem Commun. 2011. 10.1039/c0cc05671e. 21451870 · DOI
  86. [87]Szulik MW, Pallan PS, Nocek B, Voehler M, Banerjee S, Brooks S, et al. Differential Stabilities and Sequence-Dependent Base Pair Opening Dynamics of Watson–Crick Base Pairs with 5-Hydroxymethylcytosine, 5-Formylcytosine, or 5-Carboxylcytosine. Biochemistry. 2015. 10.1021/bi501534x. 25632825 PMC4325598 · DOI
  87. [88]Arango D, Sturgill D, Alhusaini N, Dillman AA, Sweet TJ, Hanson G, et al. Acetylation of Cytidine in mRNA Promotes Translation Efficiency. Cell. 2018. 10.1016/j.cell.2018.10.030. 30449621 PMC6295233 · DOI · Paper page
  88. [89]Tardu M, Jones JD, Kennedy RT, Lin Q, Koutmou KS. Identification and Quantification of Modified Nucleosides in Saccharomyces cerevisiae mRNAs. ACS Chem Biol. 2019. 10.1021/acschembio.9b00369. 31243956 PMC7254066 · DOI
  89. [90]McIntyre W, Netzband R, Bonenfant G, Biegel JM, Miller C, Fuchs G, et al. Positive-sense RNA viruses reveal the complexity and dynamics of the cellular and viral epitranscriptomes during infection. Nucleic Acids Res. 2018. 10.1093/nar/gky029. 29373715 PMC6009648 · DOI
  90. [91]Liu Y, Wang X, Liu Y, Yang J, Mao W, Feng C, et al. N4-acetylcytidine-dependent GLMP mRNA stabilization by NAT10 promotes head and neck squamous cell carcinoma metastasis and remodels tumor microenvironment through MAPK/ERK signaling pathway. Cell Death Dis. 2023. 10.1038/s41419-023-06245-6. 37914704 PMC10620198 · DOI
  91. [92]Long Y, Ren Y, Wei Q, Mobet Y, Liu Y, Zhao H, et al. NAT10-mediated RNA acetylation enhances HNRNPUL1 mRNA stability to contribute cervical cancer progression. Int J Med Sci. 2023. 10.7150/ijms.83828. 37484809 PMC10357443 · DOI
  92. [93]Hao H, Liu W, Miao Y, Ma L, Yu B, Liu L, et al. N4-acetylcytidine regulates the replication and pathogenicity of enterovirus 71. Nucleic Acids Res. 2022. 10.1093/nar/gkac675. 35971620 PMC9458434 · DOI
  93. [94]Tsai K, Jaguva Vasudevan AA, Martinez Campos C, Emery A, Swanstrom R, Cullen BR. Acetylation of Cytidine Residues Boosts HIV-1 Gene Expression by Increasing Viral RNA Stability. Cell Host Microbe. 2020. 10.1016/j.chom.2020.05.011. 32533923 PMC7429276 · DOI
  94. [95]Zhang Z, Chen L-Q, Zhao Y-L, Yang C-G, Roundtree IA, Zhang Z, et al. Single-base mapping of m 6 A by an antibody-independent method. Sci Adv. 2019. 10.1126/sciadv.aax0250. 31281898 PMC6609220 · DOI
  95. [96]Bartee D, Nance KD, Meier JL. Site-Specific Synthesis of N 4 -Acetylcytidine in RNA Reveals Physiological Duplex Stabilization. J Am Chem Soc. 2022. 10.1021/jacs.1c11985. 35172571 PMC11583671 · DOI
  96. [97]Parthasarathy R, Ginell SL, De NC, Chheda GB. Conformation of N4-acetylcytidine, a modified nucleoside of tRNA, and stereochemistry of codon-anticodon interaction. Biochem Biophys Res Commun. 1978. 10.1016/0006-291X(78)91040-9. 697848 · DOI
  97. [98]Kumbhar BV, Kamble AD, Sonawane KD. Conformational Preferences of Modified Nucleoside N(4)-Acetylcytidine, ac4C Occur at Wobble 34th Position in the Anticodon Loop of tRNA. Cell Biochem Biophys. 2013. 10.1007/s12013-013-9525-8. 23408308 · DOI
  98. [99]Wang W, Liu H, Wang F, Liu X, Sun Y, Zhao J, et al. N4-acetylation of cytidine in mRNA plays essential roles in plants. Plant Cell. 2023. 10.1093/plcell/koad189. 37367221 PMC10533332 · DOI
  99. [100]Schwartz S, Bernstein DA, Mumbach MR, Jovanovic M, Herbst RH, León-Ricardo BX, et al. Transcriptome-wide Mapping Reveals Widespread Dynamic-Regulated Pseudouridylation of ncRNA and mRNA. Cell. 2014. 10.1016/j.cell.2014.08.028. 25219674 PMC4180118 · DOI
  100. [101]Charette M, Gray MW. Pseudouridine in RNA: What, Where, How, and Why. IUBMB Life. 2000. 10.1080/152165400410182. 10902565 · DOI
  101. [102]Li X, Zhu P, Ma S, Song J, Bai J, Sun F, et al. Chemical pulldown reveals dynamic pseudouridylation of the mammalian transcriptome. Nat Chem Biol. 2015. 10.1038/nchembio.1836. 26075521 · DOI
  102. [103]Li X, Ma S, Yi C. Pseudouridine: the fifth RNA nucleotide with renewed interests. Curr Opin Chem Biol. 2016. 10.1016/j.cbpa.2016.06.014. 27348156 · DOI
  103. [104]Ge J, Yu Y-T. RNA pseudouridylation: new insights into an old modification. Trends Biochem Sci. 2013. 10.1016/j.tibs.2013.01.002. 23391857 PMC3608706 · DOI
  104. [105]NEWBY MI, GREENBAUM NL. A conserved pseudouridine modification in eukaryotic U2 snRNA induces a change in branch-site architecture. RNA. 2001. 10.1017/S1355838201002308. 11424937 PMC1370140 · DOI
  105. [106]Newby MI, Greenbaum NL. Investigation of Overhauser effects between pseudouridine and water protons in RNA helices. Proc Natl Acad Sci. 2002. 10.1073/pnas.202477199. PMC130523 12242344 · DOI
  106. [107]Nakamoto MA, Lovejoy AF, Cygan AM, Boothroyd JC. mRNA pseudouridylation affects RNA metabolism in the parasite Toxoplasma gondii. RNA. 2017. 10.1261/rna.062794.117. 28851751 PMC5689004 · DOI
  107. [108]Karikó K, Muramatsu H, Welsh FA, Ludwig J, Kato H, Akira S, et al. Incorporation of Pseudouridine Into mRNA Yields Superior Nonimmunogenic Vector With Increased Translational Capacity and Biological Stability. Mol Ther. 2008. 10.1038/mt.2008.200. 18797453 PMC2775451 · DOI · Paper page
  108. [109]Kierzek E, Malgowska M, Lisowiec J, Turner DH, Gdaniec Z, Kierzek R. The contribution of pseudouridine to stabilities and structure of RNAs. Nucleic Acids Res. 2014. 10.1093/nar/gkt1330. 24369424 PMC3950712 · DOI · Paper page
  109. [110]Martin TW, Derewenda ZS. The name is bond—H bond. Nat Struct Biol. 1999. 10.1038/8195. 10331860 · DOI
  110. [112]Brand RC, Klootwijk J, Planta RJ, Maden BEH. Biosynthesis of a hypermodified nucleotide in Saccharomyces carlsbergensis 17S and HeLa-cell 18S ribosomal ribonucleic acid. Biochem J. 1978. 10.1042/bj1690071. 629754 PMC1184195 · DOI
  111. [113]Edmonds CG, Crain PF, Gupta R, Hashizume T, Hocart CH, Kowalak JA, et al. Posttranscriptional modification of tRNA in thermophilic archaea (Archaebacteria). J Bacteriol. 1991. 10.1128/jb.173.10.3138-3148.1991. 1708763 PMC207908 · DOI
  112. [114]Wurm JP, Meyer B, Bahr U, Held M, Frolow O, Kötter P, et al. The ribosome assembly factor Nep1 responsible for Bowen–Conradi syndrome is a pseudouridine-N1-specific methyltransferase. Nucleic Acids Res. 2010. 10.1093/nar/gkp1189. 20047967 PMC2853112 · DOI
  113. [115]Dutta N, Deb I, Sarzynska J, Lahiri A. Structural and thermodynamic consequences of base pairs containing pseudouridine and N1-methylpseudouridine in RNA duplexes. ChemistrySelect. 2025. 10.1002/slct.202400006. · DOI
  114. [116]Ding Y, Tang Y, Kwok CK, Zhang Y, Bevilacqua PC, Assmann SM. In vivo genome-wide profiling of RNA secondary structure reveals novel regulatory features. Nature. 2014. 10.1038/nature12756. 24270811 · DOI · Paper page
  115. [119]Andries O, Mc Cafferty S, De Smedt SC, Weiss R, Sanders NN, Kitada T. N1-methylpseudouridine-incorporated mRNA outperforms pseudouridine-incorporated mRNA by providing enhanced protein expression and reduced immunogenicity in mammalian cell lines and mice. J Controlled Release. 2015. 10.1016/j.jconrel.2015.08.051. 26342664 · DOI · Paper page
  116. [120]Murao K, Ishikura H, Albani M, Kersten H. On the biosynthesis of 5-methoxyuridine and uridine-5-oxyacetic acid in specific procaryotic transfer RNAs. Nucleic Acids Res. 1978. 10.1093/nar/5.4.1273. 418384 PMC342075 · DOI
  117. [121]Sheng J, Zhang W, Hassan AEA, Gan J, Soares AS, Geng S, et al. Hydrogen bond formation between the naturally modified nucleobase and phosphate backbone. Nucleic Acids Res. 2012. 10.1093/nar/gks426. 22641848 PMC3439885 · DOI
  118. [122]Li B, Luo X, Dong Y. Effects of Chemically Modified Messenger RNA on Protein Expression. Bioconjug Chem. 2016. 10.1021/acs.bioconjchem.6b00090. 26906521 · DOI
  119. [123]Takeda N, Nakamura M, Yoshizumi H, Tatematsu A. Detection of ribose-methylated nucleotides in Pyrodictium occultum tRNA by liquid chromatography—frit-fast atom bombardment mass spectrometry. J Chromatogr B Biomed Sci Appl. 1994. 10.1016/0378-4347(94)00299-1. 7866511 · DOI
  120. [124]Droogmans L, Grosjean H. 2′-O-methylation and inosine formation in the wobble position of anticodon-substituted tRNA-Phe in a homologous yeast in vitro system. Biochimie. 1991. 10.1016/0300-9084(91)90143-O. 1742347 · DOI
  121. [125]Taoka M, Nobe Y, Yamaki Y, Sato K, Ishikawa H, Izumikawa K, et al. Landscape of the complete RNA chemical modifications in the human 80S ribosome. Nucleic Acids Res. 2018. 10.1093/nar/gky811. 30202881 PMC6182160 · DOI
  122. [126]Krogh N, Kongsbak-Wismann M, Geisler C, Nielsen H. Substoichiometric ribose methylations in spliceosomal snRNAs. Org Biomol Chem. 2017. 10.1039/C7OB02317K. 29048444 · DOI
  123. [127]Dai Q, Moshitch-Moshkovitz S, Han D, Kol N, Amariglio N, Rechavi G, et al. Nm-seq maps 2′-O-methylation sites in human mRNA with base precision. Nat Methods. 2017. 10.1038/nmeth.4294. 28504680 PMC5712428 · DOI
  124. [128]Elliott BA, Ho H-T, Ranganathan SV, Vangaveti S, Ilkayeva O, Abou Assi H, et al. Modification of messenger RNA by 2′-O-methylation regulates gene expression in vivo. Nat Commun. 2019. 10.1038/s41467-019-11375-7. 31363086 PMC6667457 · DOI
  125. [129]Karunatilaka KS, Rueda D. Post-transcriptional modifications modulate conformational dynamics in human U2–U6 snRNA complex. RNA. 2014. 10.1261/rna.041806.113. 24243115 PMC3866641 · DOI
  126. [130]Somme J, Van Laer B, Roovers M, Steyaert J, Versées W, Droogmans L. Characterization of two homologous 2′-O-methyltransferases showing different specificities for their tRNA substrates. RNA. 2014. 10.1261/rna.044503.114. 24951554 PMC4105751 · DOI
  127. [131]Cavaillé J, Nicoloso M, Bachellerie J-P. Targeted ribose methylation of RNA in vivo directed by tailored antisense RNA guides. Nature. 1996. 10.1038/383732a0. 8878486 · DOI
  128. [132]Furuichi Y. Discovery of m7G-cap in eukaryotic mRNAs. Proc Jpn Acad Ser B Phys Biol Sci. 2015. 10.2183/pjab.91.394. PMC4729855 26460318 · DOI
  129. [133]Ayadi L, Galvanin A, Pichot F, Marchand V, Motorin Y. RNA ribose methylation (2′-O-methylation): Occurrence, biosynthesis and biological functions. Biochim et Biophys Acta (BBA) - Gene Regul Mech. 2019. 10.1016/j.bbagrm.2018.11.009. 30572123 · DOI
  130. [134]You C, Dai X, Wang Y. Position-dependent effects of regioisomeric methylated adenine and guanine ribonucleosides on translation. Nucleic Acids Res. 2017. 10.1093/nar/gkx515. 28591780 PMC5587754 · DOI
  131. [135]Kumar S, Mapa K, Maiti S. Understanding the Effect of Locked Nucleic Acid and 2′- O -Methyl Modification on the Hybridization Thermodynamics of a miRNA–mRNA Pair in the Presence and Absence of AfPiwi Protein. Biochemistry. 2014. 10.1021/bi401677d. 24564489 · DOI
  132. [136]Lane BG, Tamaoki T. Studies of the chain termini and alkali-stable dinucleotide sequences in 16 s and 28 s ribosomal RNA from L Cells. J Mol Biol. 1967. 10.1016/0022-2836(67)90024-1. 6048985 · DOI
  133. [137]Trim AR, Parker JE. Preparation, purification and analyses of thirteen alkali-stable dinucleotides from ribonucleic acid. Biochem J. 1970. 10.1042/bj1160589. 5435489 PMC1185404 · DOI
  134. [138]Abou Assi H, Rangadurai AK, Shi H, Liu B, Clay MC, Erharter K, et al. 2′- O -Methylation can increase the abundance and lifetime of alternative RNA conformational states. Nucleic Acids Res. 2020. 10.1093/nar/gkaa928. 33104789 PMC7708057 · DOI
  135. [139]Cummins LL, Owens SR, Risen LM, Lesnik EA, Freier SM, McGee D, et al. Characterization of fully 2’-modified oligoribonucleotide hetero- and homoduplex hybridization and nuclease sensitivity. Nucleic Acids Res. 1995. 10.1093/nar/23.11.2019. 7541132 PMC306978 · DOI
  136. [140]Majlessi M. Advantages of 2’-O-methyl oligoribonucleotide probes for detecting RNA targets. Nucleic Acids Res. 1998. 10.1093/nar/26.9.2224. 9547284 PMC147516 · DOI
  137. [141]Kawai G, Yamamoto Y, Kamimura T, Masegi T, Sekine M, Hata T, et al. Conformational rigidity of specific pyrimidine residues in tRNA arises from posttranscriptional modifications that enhance steric interaction between the base and the 2’-hydroxyl group. Biochemistry. 1992. 10.1021/bi00119a012. 1310418 · DOI
  138. [142]Yildirim I, Kierzek E, Kierzek R, Schatz GC. Interplay of LNA and 2′- O -Methyl RNA in the Structure and Thermodynamics of RNA Hybrid Systems: A Molecular Dynamics Study Using the Revised AMBER Force Field and Comparison with Experimental Results. J Phys Chem B. 2014. 10.1021/jp506703g. 25268896 · DOI
  139. [143]Ji L, Chen X. Regulation of small RNA stability: methylation and beyond. Cell Res. 2012. 10.1038/cr.2012.36. 22410795 PMC3317568 · DOI
  140. [144]Liang H, Jiao Z, Rong W, Qu S, Liao Z, Sun X, et al. 3′-Terminal 2′-O-methylation of lung cancer miR-21-5p enhances its stability and association with Argonaute 2. Nucleic Acids Res. 2020. 10.1093/nar/gkaa504. 32542340 PMC7367198 · DOI
  141. [145]Kowalak JA, Dalluge JJ, McCloskey JA, Stetter KO. The Role of Posttranscriptional Modification in Stabilization of Transfer RNA from Hyperthermophiles. Biochemistry. 1994. 10.1021/bi00191a014. 7516708 · DOI
  142. [146]Guymon R, Pomerantz SC, Crain PF, McCloskey JA. Influence of Phylogeny on Posttranscriptional Modification of rRNA in Thermophilic Prokaryotes: The Complete Modification Map of 16S rRNA of Thermus thermophilus. Biochemistry. 2006. 10.1021/bi052579p. 16605256 · DOI
  143. [147]Dennis PP, Tripp V, Lui L, Lowe T, Randau L. C/D box sRNA-guided 2′-O-methylation patterns of archaeal rRNA molecules. BMC Genomics. 2015. 10.1186/s12864-015-1839-z. 26296872 PMC4644070 · DOI
  144. [148]Xiong J, Wu J, Liu Y, Feng Y-J, Yuan B-F. Quantification and mapping of RNA modifications. TRAC Trends Anal Chem. 2024. 10.1016/j.trac.2024.117606. · DOI
  145. [149]Ke S, Alemu EA, Mertens C, Gantman EC, Fak JJ, Mele A, et al. A majority of m 6 A residues are in the last exons, allowing the potential for 3′ UTR regulation. Genes Dev. 2015. 10.1101/gad.269415.115. 26404942 PMC4604345 · DOI
  146. [150]Chen K, Lu Z, Wang X, Fu Y, Luo G, Liu N, et al. High-Resolution N 6 ‐Methyladenosine (m 6 A) Map Using Photo‐Crosslinking‐Assisted m 6 A Sequencing. Angew Chem. 2015. 10.1002/ange.201410647. PMC4396828 25491922 · DOI
  147. [151]Horowitz S, Horowitz A, Nilsen TW, Munns TW, Rottman FM. Mapping of N6-methyladenosine residues in bovine prolactin mRNA. Proc Natl Acad Sci. 1984. 10.1073/pnas.81.18.5667. 6592581 PMC391771 · DOI
  148. [152]Narayan P, Ludwiczak RL, Goodwin EC, Rottman FM. Context effects on N 6 -adenosine methylation sites in prolactin mRNA. Nucleic Acids Res. 1994. 10.1093/nar/22.3.419. 8127679 PMC523598 · DOI
  149. [153]Liu J, Li K, Cai J, Zhang M, Zhang X, Xiong X, et al. Landscape and Regulation of m6A and m6Am Methylome across Human and Mouse Tissues. Mol Cell. 2020. 10.1016/j.molcel.2019.09.032. 31676230 · DOI
  150. [154]Lin S, Choe J, Du P, Triboulet R, Gregory RI. The m 6 A Methyltransferase METTL3 Promotes Translation in Human Cancer Cells. Mol Cell. 2016. 10.1016/j.molcel.2016.03.021. 27117702 PMC4860043 · DOI · Paper page
  151. [155]Li A, Chen Y-S, Ping X-L, Yang X, Xiao W, Yang Y, et al. Cytoplasmic m6A reader YTHDF3 promotes mRNA translation. Cell Res. 2017. 10.1038/cr.2017.10. 28106076 PMC5339832 · DOI
  152. [156]Shi H, Wang X, Lu Z, Zhao BS, Ma H, Hsu PJ, et al. YTHDF3 facilitates translation and decay of N6-methyladenosine-modified RNA. Cell Res. 2017. 10.1038/cr.2017.15. 28106072 PMC5339834 · DOI · Paper page
  153. [157]Coots RA, Liu X-M, Mao Y, Dong L, Zhou J, Wan J, et al. m6A Facilitates eIF4F-Independent mRNA Translation. Mol Cell. 2017. 10.1016/j.molcel.2017.10.002. 29107534 PMC5913006 · DOI
  154. [158]Meyer KD, Patil DP, Zhou J, Zinoviev A, Skabkin MA, Elemento O, et al. 5′ UTR m6A Promotes Cap-Independent Translation. Cell. 2015. 10.1016/j.cell.2015.10.012. 26593424 PMC4695625 · DOI
  155. [159]Choi J, Ieong K-W, Demirci H, Chen J, Petrov A, Prabhakar A, et al. N6-methyladenosine in mRNA disrupts tRNA selection and translation-elongation dynamics. Nat Struct Mol Biol. 2016. 10.1038/nsmb.3148. 26751643 PMC4826618 · DOI
  156. [160]Liu B, Merriman DK, Choi SH, Schumacher MA, Plangger R, Kreutz C, et al. A potentially abundant junctional RNA motif stabilized by m6A and Mg2+. Nat Commun. 2018. 10.1038/s41467-018-05243-z. 30018356 PMC6050335 · DOI
  157. [161]Luo J-H, Wang Y, Wang M, Zhang L-Y, Peng H-R, Zhou Y-Y, et al. Natural Variation in RNA m 6 A Methylation and Its Relationship with Translational Status. Plant Physiol. 2020. 10.1104/pp.19.00987. 31591151 PMC6945879 · DOI
  158. [162]Huang T, He W-J, Li C, Zhang J-B, Liao Y-C, Song B, et al. Transcriptome-wide analyses of RNA m6A methylation in hexaploid wheat reveal its roles in mRNA translation regulation. Front Plant Sci. 2022. 10.3389/fpls.2022.917335. 36092414 PMC9453602 · DOI
  159. [163]Huang T, Chen W, Liu J, Gu N, Zhang R. Genome-wide identification of mRNA 5-methylcytosine in mammals. Nat Struct Mol Biol. 2019. 10.1038/s41594-019-0218-x. 31061524 · DOI
  160. [164]Ma H-L, Bizet M, Soares Da Costa C, Murisier F, de Bony EJ, Wang M-K, et al. SRSF2 plays an unexpected role as reader of m5C on mRNA, linking epitranscriptomics to cancer. Mol Cell. 2023. 10.1016/j.molcel.2023.11.003. 38065062 PMC11090011 · DOI
  161. [165]Amort T, Rieder D, Wille A, Khokhlova-Cubberley D, Riml C, Trixl L, et al. Distinct 5-methylcytosine profiles in poly(A) RNA from mouse embryonic stem cells and brain. Genome Biol. 2017. 10.1186/s13059-016-1139-1. 28077169 PMC5225599 · DOI
  162. [166]Chen S-Y, Chen K-L, Ding L-Y, Yu C-H, Wu H-Y, Chou Y-Y, et al. RNA bisulfite sequencing reveals NSUN2-mediated suppression of epithelial differentiation in pancreatic cancer. Oncogene. 2022. 10.1038/s41388-022-02325-7. 35501460 · DOI
  163. [167]Gu X, Li P, Gao X, Ru Y, Xue C, Zhang S, et al. RNA 5-methylcytosine writer NSUN5 promotes hepatocellular carcinoma cell proliferation via a ZBED3-dependent mechanism. Oncogene. 2024. 10.1038/s41388-023-02931-z. 38182896 PMC10890930 · DOI
  164. [168]Zhang L, Li Y, Li L, Yao F, Cai M, Ye D, et al. Detection, molecular function and mechanisms of m5C in cancer. Clin Translational Med. 2025. 10.1002/ctm2.70239. PMC11862898 40008496 · DOI
  165. [169]Selmi T, Hussain S, Dietmann S, Heiß M, Borland K, Flad S, et al. Sequence- and structure-specific cytosine-5 mRNA methylation by NSUN6. Nucleic Acids Res. 2021. 10.1093/nar/gkaa1193. 33330931 PMC7826283 · DOI
  166. [170]Liu J, Huang T, Zhang Y, Zhao T, Zhao X, Chen W, et al. Sequence- and structure-selective mRNA m5C methylation by NSUN6 in animals. Natl Sci Rev. 2021. 10.1093/nsr/nwaa273. 34691665 PMC8288183 · DOI
  167. [171]Liu J, Huang T, Chen W, Ding C, Zhao T, Zhao X, et al. Developmental mRNA m5C landscape and regulatory innovations of massive m5C modification of maternal mRNAs in animals. Nat Commun. 2022. 10.1038/s41467-022-30210-0. 35513466 PMC9072368 · DOI
  168. [172]Lu L, Zhang X, Zhou Y, Shi Z, Xie X, Zhang X, et al. Base-resolution m5C profiling across the mammalian transcriptome by bisulfite-free enzyme-assisted chemical labeling approach. Mol Cell. 2024. 10.1016/j.molcel.2024.06.021. 39002544 · DOI
  169. [173]Li W, Li X, Ma X, Xiao W, Zhang J. Mapping the m1A, m5C, m6A and m7G methylation atlas in zebrafish brain under hypoxic conditions by MeRIP-seq. BMC Genomics. 2022. 10.1186/s12864-022-08350-w. 35135476 PMC8822802 · DOI
  170. [174]Tang H, Fan X, Xing J, Liu Z, Jiang B, Dou Y, et al. NSun2 delays replicative senescence by repressing p27 (KIP1) translation and elevating CDK1 translation. Aging. 2015. 10.18632/aging.100860. 26687548 PMC4712338 · DOI
  171. [175]Xing J, Yi J, Cai X, Tang H, Liu Z, Zhang X, et al. NSun2 Promotes Cell Growth via Elevating Cyclin-Dependent Kinase 1 Translation. Mol Cell Biol. 2015. 10.1128/MCB.00742-15. 26391950 PMC4628067 · DOI
  172. [176]Schumann U, Zhang H-N, Sibbritt T, Pan A, Horvath A, Gross S, et al. Multiple links between 5-methylcytosine content of mRNA and translation. BMC Biol. 2020. 10.1186/s12915-020-00769-5. 32293435 PMC7158060 · DOI
  173. [177]Wang N, Tang H, Wang X, Wang W, Feng J. Homocysteine upregulates interleukin-17A expression via NSun2-mediated RNA methylation in T lymphocytes. Biochem Biophys Res Commun. 2017. 10.1016/j.bbrc.2017.09.069. 28919411 · DOI
  174. [178]Li Q, Li X, Tang H, Jiang B, Dou Y, Gorospe M, et al. NSUN2-Mediated m5C Methylation and METTL3/METTL14-Mediated m6A Methylation Cooperatively Enhance p21 Translation. J Cell Biochem. 2017. 10.1002/jcb.25957. 28247949 PMC5509477 · DOI
  175. [179]Yang L, Ren Z, Yan S, Zhao L, Liu J, Zhao L, et al. Nsun4 and Mettl3 mediated translational reprogramming of Sox9 promotes BMSC chondrogenic differentiation. Commun Biology. 2022. 10.1038/s42003-022-03420-x. PMC9133052 35614315 · DOI
  176. [180]Hoernes TP, Heimdörfer D, Köstner D, Faserl K, Nußbaumer F, Plangger R, et al. Eukaryotic Translation Elongation is Modulated by Single Natural Nucleotide Derivatives in the Coding Sequences of mRNAs. Genes. 2019. 10.3390/genes10020084. 30691071 PMC6409545 · DOI
  177. [181]Delatte B, Wang F, Ngoc LV, Collignon E, Bonvin E, Deplus R, et al. Transcriptome-wide distribution and function of RNA hydroxymethylcytosine. Science. 2016. 10.1126/science.aac5253. 26816380 · DOI
  178. [182]Miao Z, Xin N, Wei B, Hua X, Zhang G, Leng C, et al. 5-hydroxymethylcytosine is detected in RNA from mouse brain tissues. Brain Res. 2016. 10.1016/j.brainres.2016.04.055. 27117867 · DOI
  179. [183]Zhou HQ, Zhu Z, Zhang JW, Lin WP, Jin HJ, Ding YY, et al. Dynamic regulation of mRNA acetylation at synapses by spatial memory in mouse hippocampus. 2024. Preprint at: https://www.biorxiv.org/lookup/doi/10.1101/2024.06.01.596932?__cf_chl_rt_tk=VCWCBxxPoCSyi6JKVc5ZfHIbW3j5xqinfmlzZ_fDx4E-1761149982-1.0.1.1-XBoD6wTdzHWI7faONvWcnKQQPwbUsVaYKFDvFZiV7Oo. PMC13008358 41870036 · DOI
  180. [184]Xu L, Zheng S, Liu B, Xu C, Yang L, Zhou Q, et al. Epitranscriptomic profiling of N4-acetylcytidine-related RNA acetylation in the spinal dorsal horn of rat with cancer-induced bone pain. Mol Pain. 2023. 10.1177/17448069231178487. 37211783 PMC10204061 · DOI
  181. [185]Xu T, Wang J, Wu Y, Wu J, Lu W, Liu M, et al. Ac4C Enhances the Translation Efficiency of Vegfa mRNA and Mediates Central Sensitization in Spinal Dorsal Horn in Neuropathic Pain. Adv Sci. 2023. 10.1002/advs.202303113. PMC10724395 37877615 · DOI
  182. [186]Arango D, Sturgill D, Yang R, Kanai T, Bauer P, Roy J, et al. Direct epitranscriptomic regulation of mammalian translation initiation through N4-acetylcytidine. Mol Cell. 2022. 10.1016/j.molcel.2022.05.016. 35931039 PMC9365200 · DOI
  183. [187]Lu X, He Y, Guo J-Q, Wang Y, Yan Q, Xiong Q, et al. Dynamics of epitranscriptomes uncover translational reprogramming directed by ac4C in rice during pathogen infection. Nat Plants. 2024. 10.1038/s41477-024-01800-1. 39317771 · DOI
  184. [188]Liu R, Wubulikasimu Z, Cai R, Meng F, Cui Q, Zhou Y, et al. NAT10-mediated N4-acetylcytidine mRNA modification regulates self-renewal in human embryonic stem cells. Nucleic Acids Res. 2023. 10.1093/nar/gkad628. 37497776 PMC10484679 · DOI
  185. [189]Yan Q, Zhou J, Wang Z, Ding X, Ma X, Li W, et al. NAT10-dependent N4-acetylcytidine modification mediates PAN RNA stability, KSHV reactivation, and IFI16-related inflammasome activation. Nat Commun. 2023. 10.1038/s41467-023-42135-3. 37816771 PMC10564894 · DOI
  186. [190]Nance KD, Gamage ST, Alam MM, Yang A, Levy MJ, Link CN, et al. Cytidine acetylation yields a hypoinflammatory synthetic messenger RNA. Cell Chem Biology. 2022. 10.1016/j.chembiol.2021.07.003. PMC10370389 35180432 · DOI
  187. [191]Carlile TM, Rojas-Duran MF, Zinshteyn B, Shin H, Bartoli KM, Gilbert WV. Pseudouridine profiling reveals regulated mRNA pseudouridylation in yeast and human cells. Nature. 2014. 10.1038/nature13802. 25192136 PMC4224642 · DOI
  188. [192]Sun L, Xu Y, Bai S, Bai X, Zhu H, Dong H, et al. Transcriptome-wide analysis of pseudouridylation of mRNA and non-coding RNAs in Arabidopsis. J Exp Bot. 2019. 10.1093/jxb/erz273. 31173101 PMC6793436 · DOI
  189. [193]Huang S, Wylder AC, Pan T. Simultaneous nanopore profiling of mRNA m6A and pseudouridine reveals translation coordination. Nat Biotechnol. 2024. 10.1038/s41587-024-02135-0. 38321115 PMC11300707 · DOI
  190. [194]Karikó K, Muramatsu H, Keller JM, Weissman D. Increased Erythropoiesis in Mice Injected With Submicrogram Quantities of Pseudouridine-containing mRNA Encoding Erythropoietin. Mol Ther. 2012. 10.1038/mt.2012.7. 22334017 PMC3345990 · DOI · Paper page
  191. [195]Hall KB, McLaughlin LW. Properties of pseudouridine N1 imino protons located in the major groove of an A-form RNA duplex. Nucleic Acids Res. 1992. 10.1093/nar/20.8.1883. 1579489 PMC312302 · DOI
  192. [196]Karijolich J, Yu Y-T. Converting nonsense codons into sense codons by targeted pseudouridylation. Nature. 2011. 10.1038/nature10165. 21677757 PMC3381908 · DOI
  193. [197]Pan Y, Kierzek E, Kierzek R, Mathews DH, Yu Y-T. Targeted Pseudouridylation Identifies a Novel Ψ-Ψ Codon-Anticodon Pairing in Nonsense Suppression and Translational Recoding. Nat Chem Biol. 2025. 10.1038/s41589-025-02025-9. 40940556 · DOI
  194. [198]Eyler DE, Franco MK, Batool Z, Wu MZ, Dubuke ML, Dobosz-Bartoszek M, et al. Pseudouridinylation of mRNA coding sequences alters translation. Proc Natl Acad Sci. 2019. 10.1073/pnas.1821754116. PMC6859337 31672910 · DOI
  195. [199]Chen T-H, Potapov V, Dai N, Ong JL, Roy B. N1-methyl-pseudouridine is incorporated with higher fidelity than pseudouridine in synthetic RNAs. Sci Rep. 2022. 10.1038/s41598-022-17249-1. 35906281 PMC9335462 · DOI
  196. [200]Monroe J. N1-methylpseudouridine and pseudouridine mRNA modifications modulate translation rate and fidelity. 2022. https://deepblue.lib.umich.edu/bitstream/handle/2027.42/174506/monroejg_1.pdf. Accessed 15 Jul 2025. PMC11405884 39284850
  197. [201]Parr CJC, Wada S, Kotake K, Kameda S, Matsuura S, Sakashita S, et al. N 1-Methylpseudouridine substitution enhances the performance of synthetic mRNA switches in cells. Nucleic Acids Res. 2020. 10.1093/nar/gkaa070. 32090264 PMC7102939 · DOI
  198. [202]Chen S, Liu Z, Cai J, Li H, Qiu M. N1-methylpseudouridine modification level correlates with protein expression, immunogenicity, and stability of mRNA. MedComm. 2024. 10.1002/mco2.691. 39290255 PMC11406044 · DOI
  199. [203]Kim KQ, Burgute BD, Tzeng S-C, Jing C, Jungers C, Zhang J, et al. N1-methylpseudouridine found within COVID-19 mRNA vaccines produces faithful protein products. Cell Rep. 2022. 10.1016/j.celrep.2022.111300. 35988540 PMC9376333 · DOI
  200. [204]Mulroney TE, Pöyry T, Yam-Puc JC, Rust M, Harvey RF, Kalmar L, et al. N1-methylpseudouridylation of mRNA causes + 1 ribosomal frameshifting. Nature. 2024. 10.1038/s41586-023-06800-3. 38057663 PMC10764286 · DOI

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Cited by

Sorted by citations

Authors
Kukushkina-Zvezdova, A. A., Zherebtsova, A. A., Telegina, D. V., Skvortsov, I. A., Ivanov, R. A., & Reshetnikov, V. V.
Affiliations
Sirius University of Science and Technology (RU)
Corresponding author
Reshetnikov, Vasiliy V.
Venue
Journal of Translational Medicine
Published
2026-04-07
Volume
24
Issue
1
ISSN
1479-5876 (ISSN-L)
OpenAlex
W7150822187
Cited by
3
References
25
Citations by year
2026: 3
FWCI
1.79
Type
journal article
Language
en
Open access
Locations
  • Journal of Translational Medicine (publishedVersion, cc-by-nc-nd)
  • PubMed (publishedVersion)
  • PubMed Central (publishedVersion, cc-by-nc-nd)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
Funders
«Sirius» Federal Territory (Agreement № 3-03 date February 18, 2025)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Interference and Gene Delivery
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA modifications and cancer
Keywords
mRNA therapeutics, nucleoside analogues, modified nucleosides, mRNA stability, pseudouridine, N1-methylpseudouridine, mRNA translation, immunogenicity, mRNA vaccines, gene replacement therapy, cancer therapy
MeSH terms
Animals, Humans, Nucleosides, RNA, RNA, Messenger, RNA Stability

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